In Stranger Things, the Mind Flayer is a pretty big deal, as it is essentially the brain of the Upside Down, or at least some elements of it. For instance, it is responsible for spread the vines beneath Hawkins. It can also control the demo-dogs, as well as Will.
So it is safe to assume it can control all or most of the Upside Down. That being said, where was it in Season 1? All those times the vines where getting burnt, and the Demogorgon getting hurt.